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Sample GSM659355 Query DataSets for GSM659355
Status Public on Jun 15, 2011
Title HCT-116 si TUT1 replicate 2 canonical assay
Sample type RNA
 
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si TUT1
Treatment protocol Treated with 30 nM Dharmacon SMARTpool siRNAs against enzyme of interest or Cyclophilin B as a negative control
Growth protocol HCT-116 cells grown in McCoy's media with 10% FBS
Extracted molecule total RNA
Extraction protocol RNA was isolated using the miRNeasy RNA isolation kit from Qiagen. 400 ng of RNA was used as input for the nCounter sample prep reaction.
Label N/A
Label protocol N/A
 
Hybridization protocol Hybrdization reactions were performed according to the manufacturer's instructions (NanoString) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.
Scan protocol Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed.
Description Canonical
Replicate 2
Data processing The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using the vsn R package
 
Submission date Jan 21, 2011
Last update date Jun 15, 2011
Contact name Muneesh Tewari
E-mail(s) mtewari@fhcrc.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Tewari
Street address 1100 Fairview Ave, N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL11642
Series (2)
GSE26803 Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (KD)
GSE26970 Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

Data table header descriptions
ID_REF
VALUE Normalized miRNA counts

Data table
ID_REF VALUE
hsa-miR-140-5p 26.85584973
hsa-miR-146a 20.16370665
hsa-miR-134 8.452585877
hsa-miR-128 45.25929507
hsa-miR-149 10.12557634
hsa-miR-1308 3.433929011
hsa-miR-200b 117.2001615
hsa-miR-92b 59.48015686
hsa-miR-455-5p 21.83674047
hsa-miR-34c-5p 10.96207774
hsa-miR-99b 67.84537253
hsa-let-7e 125.5653813
hsa-miR-199a-5p 3.433929011
hsa-miR-18b 16.81764526
hsa-miR-509-3p 10.96207774
hsa-miR-320a 0.926531965
hsa-miR-10b 5.106710702
hsa-let-7c 44.42277408
hsa-miR-103 294.5428405
hsa-miR-886-5p 5.943156974

Total number of rows: 125

Table truncated, full table size 2 Kbytes.




Supplementary file Size Download File type/resource
GSM659355_tut_2_canonical.RCC.gz 6.3 Kb (ftp)(http) RCC
Processed data included within Sample table

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